Schema for xenoRefGene
  Database: danRer7    Primary Table: xenoRefGene    Row Count: 271,761   Data last updated: 2020-08-21
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 590smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001005045varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr18varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 763671int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 768374int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 763671int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 768374int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 4int(10) unsigned range Number of exons
exonStarts 763671,764109,766857,768281,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 763890,764205,766965,768374,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 dhdh-like.1varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 0,0,0,0,longblob   Reading frame of the start of the CDS region of the exon, in the direction of transcription (0,1,2), or -1 if there is no CDS region.

Connected Tables and Joining Fields
        danRer7.all_est.qName (via xenoRefGene.name)
      danRer7.all_mrna.qName (via xenoRefGene.name)
      danRer7.refGene.name (via xenoRefGene.name)
      danRer7.refSeqAli.qName (via xenoRefGene.name)
      danRer7.xenoMrna.qName (via xenoRefGene.name)
      danRer7.xenoRefFlat.name (via xenoRefGene.name)
      danRer7.xenoRefSeqAli.qName (via xenoRefGene.name)
      hgFixed.gbCdnaInfo.acc (via xenoRefGene.name)
      hgFixed.gbMiscDiff.acc (via xenoRefGene.name)
      hgFixed.gbSeq.acc (via xenoRefGene.name)
      hgFixed.gbWarn.acc (via xenoRefGene.name)
      hgFixed.imageClone.acc (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
590NM_001005045chr18-7636717683747636717683744763671,764109,766857,768281,763890,764205,766965,768374,0dhdh-like.1cmplincmpl0,0,0,0,
664NM_001004945chr18+10379401104007931037940110400793710379401,10380047,10380303,10380606,10383264,10384898,10400625,10379491,10380211,10380307,10380696,10383360,10384954,10400793,0ttc38incmplincmpl0,0,2,0,0,0,0,
657NM_001359227chr6+9500606953086595006069527686179500606,9504576,9504807,9510832,9511061,9513887,9518650,9518969,9519250,9522044,9522151,9523090,9524600,9524798,9524967,9527614, ...9500657,9504657,9504888,9510892,9511175,9513983,9518883,9519059,9519256,9522147,9522154,9523162,9524670,9524887,9525054,9527686, ...0Slc44a2incmplincmpl0,0,0,0,0,0,0,2,2,2,0,0,0,1,0,0,-1,
858NM_111692chr9-35838496358431833583849635843183435838496,35840954,35841107,35843093,35838556,35841050,35841236,35843183,0AAC1incmplincmpl0,0,0,0,
595NM_001245769chr14-135837313640111358373136401151358373,1360559,1361345,1361393,1363932,1358445,1360695,1361347,1361522,1364011,0LOC100190443incmplincmpl1,2,0,0,2,
726NM_001245769chr14+18562885185650361856288518565036318562885,18563693,18564940,18563020,18563825,18565036,0LOC100190443incmplincmpl0,0,0,
681NM_001311011chr18+12660465126684211266054212668421912660465,12664928,12665168,12666303,12666450,12666482,12667586,12667946,12668337,12660549,12665076,12665287,12666379,12666452,12666599,12667691,12668027,12668421,0zgc:56622cmplincmpl0,0,1,0,1,0,0,0,0,
655NM_001310909chr19+922954992302229229552923022229229549,9230093,9229693,9230222,0s100a10acmplincmpl0,0,
752NM_001310899chr7-21998387220035432199838722003543521998387,21999602,22002660,22002830,22003503,21998476,21999708,22002737,22002968,22003543,0fis1cmplincmpl1,0,1,1,0,
917NM_001322176chr11-43600926436043014360092643604301343600926,43601607,43604238,43601436,43601799,43604301,0PDE12incmplincmpl0,0,0,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.